Mike J,
on my 2002 Marquis, I had a battery isolator that was mounted just above the batteries in the left rear battery compartment. Did not have a solenoid that tied the batteries together that is in your schematic. Possibly one or both of the diodes failed in the isolator. Possibly miswired at isolator. There are 3 terminals on the isolator, middle one is from the altanator, the outside two go to each set of batteries. If you have a Echo Charger, it will be wired into the isolator as well. This might be a good place to start troubleshooting. Hope this helps,
Frank.